Whole-genome characterization and phylogenetic analysis of Equine Rotavirus A isolated from Jeju Island, Korea.

Overview

• This study reports the first complete genome characterization of Equine Rotavirus A (ERVA) from Jeju Island, Korea, and analyzes its genetic relationship with global ERVA strains to understand virus diversity and transmission patterns.

Introduction and Background

• Equine Rotavirus A (ERVA) is a leading cause of acute diarrhea in newborn foals, which can lead to considerable economic losses in the equine industry due to illness and mortality.
• ERVA exhibits genetic variation and diverse global transmission routes, complicating efforts to control and prevent outbreaks through vaccines and management strategies.
• Understanding the full genome composition and evolutionary relationships of ERVA strains is critical for guiding vaccine design and epidemiological tracking.

Objectives

• To perform a complete whole-genome sequencing of an ERVA strain isolated from Jeju Island, Korea.
• To analyze the genotypic composition and phylogenetic relationships of this Korean isolate in comparison to other global ERVA strains.

Methods

• Sample Collection:
  • Twenty-five fecal and swab samples were collected from diarrheic horses on Jeju Island during spring and summer of 2025.
• Screening:
  • Samples were screened for ERVA by antigen testing and reverse transcription polymerase chain reaction (RT-PCR).
  • One sample that tested positive by both methods was selected for further analysis.
• Whole-Genome Sequencing:
  • The 11 genome segments of the virus were amplified using segment-specific primers.
  • Sanger sequencing, a classical nucleotide sequencing method known for accuracy, was used to determine nucleotide sequences.
• Phylogenetic and Genetic Analysis:
  • Genome constellation, referring to the specific genotype of each of the 11 segments, was identified for the Jeju isolate.
  • Sequence identity comparisons were done to find similarities with strains from other countries.
  • Phylogenetic trees were constructed to understand evolutionary relationships and transmission patterns.

Results

• Genome Constellation:
  • The Jeju ERVA isolate showed the constellation G14-P[12]-I2-R2-C2-M3-A10-N2-T3-E2-H7, which aligns with globally common genotypes.
• Sequence Identity:
  • Most genome segments had over 99% nucleotide identity with a South African ERVA strain known as SA1.
  • The VP4 segment was an exception, showing closer similarity to a Japanese BI strain.
  • This suggests possible reassortment — a genetic mixing event where different virus strains exchange genome segments.
• Phylogenetic Analysis:
  • The Jeju isolate clustered phylogenetically with ERVA strains from South Africa and Ireland, indicating close evolutionary relationships.
  • It was distinct from recent Japanese strains, implying independent introduction and transmission routes rather than direct spread from Japan.

Conclusions and Implications

• This is the first report of the full genome sequence of ERVA from Korea, advancing knowledge about ERVA diversity in East Asia.
• The identification of a genome closely related to African and European strains indicates international circulation and complex transmission dynamics.
• The evidence of reassortment highlights the virus’s capacity to generate genetic diversity, which can complicate control efforts.
• Ongoing molecular surveillance and genome sequencing are necessary to monitor ERVA evolution, inform vaccine development, and implement effective disease prevention strategies in the Korean equine industry.